The theoretical population ecology constructs of commensalism, parasitism, and amensalism are applied in an analysis of the Knowledge Cluster Initiative (KCI), a unique social experiment establishing university-business-government alliances for knowledge-intensive innovative clusters in Japan. An analysis based on multiple negative binomial regressions to confirm the interdependence of the triple helix variables revealed that new startup venture firms served as an input factor for filing new patents and developing new products. Although the ultimate goal of the KCI was to promote new startups from the university, the startups had a commensal effect on patents and new product development. The Japanese cluster creation policy encouraged academic participation and created a mutual effect of launching new university startups. The resulting increase in the number of university researchers promoted the establishment of new startups. These startups had commensal relationships with patent applications and new product development. Although the creation of new venture startups was the ultimate goal of the cluster promotion policy, the results of this study indicate that it was the universities that benefited from the new startups that commensally contributed to increasing quantities of alliance outputs such as patents and new products.